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| -rw-r--r-- | NAMESPACE | 3 | ||||
| -rw-r--r-- | NEWS.md | 4 | ||||
| -rw-r--r-- | R/nlme.mmkin.R | 46 | ||||
| -rw-r--r-- | R/plot.nlme.mmkin.R | 6 | ||||
| -rw-r--r-- | R/sigma_twocomp.R | 21 | ||||
| -rw-r--r-- | R/summary.nlme.mmkin.R | 233 | ||||
| -rw-r--r-- | _pkgdown.yml | 1 | ||||
| -rw-r--r-- | docs/dev/news/index.html | 3 | ||||
| -rw-r--r-- | docs/dev/pkgdown.yml | 2 | ||||
| -rw-r--r-- | docs/dev/reference/Rplot001.png | bin | 27839 -> 14324 bytes | |||
| -rw-r--r-- | docs/dev/reference/index.html | 8 | ||||
| -rw-r--r-- | docs/dev/reference/nlme.mmkin.html | 96 | ||||
| -rw-r--r-- | docs/dev/reference/plot.nlme.mmkin.html | 14 | ||||
| -rw-r--r-- | docs/dev/reference/sigma_twocomp.html | 11 | ||||
| -rw-r--r-- | docs/dev/reference/summary.nlme.mmkin.html | 446 | ||||
| -rw-r--r-- | docs/dev/sitemap.xml | 3 | ||||
| -rw-r--r-- | man/nlme.mmkin.Rd | 5 | ||||
| -rw-r--r-- | man/plot.nlme.mmkin.Rd | 8 | ||||
| -rw-r--r-- | man/sigma_twocomp.Rd | 11 | ||||
| -rw-r--r-- | man/summary.nlme.mmkin.Rd | 99 | ||||
| -rw-r--r-- | test.log | 20 | ||||
| -rw-r--r-- | tests/testthat/FOCUS_2006_D.csf | 2 |
22 files changed, 949 insertions, 93 deletions
@@ -26,8 +26,10 @@ S3method(print,mmkin) S3method(print,nafta) S3method(print,nlme.mmkin) S3method(print,summary.mkinfit) +S3method(print,summary.nlme.mmkin) S3method(residuals,mkinfit) S3method(summary,mkinfit) +S3method(summary,nlme.mmkin) S3method(update,mkinfit) S3method(update,nlme.mmkin) export(CAKE_export) @@ -108,6 +110,7 @@ importFrom(stats,na.fail) importFrom(stats,nlminb) importFrom(stats,nobs) importFrom(stats,optimize) +importFrom(stats,predict) importFrom(stats,pt) importFrom(stats,qchisq) importFrom(stats,qf) @@ -1,8 +1,6 @@ # mkin 0.9.50.4 (unreleased) -- 'plot' method for 'nlme.mmkin' objects - -- 'print' method for 'mmkin' objects +- 'plot', 'summary' and 'print' methods for 'nlme.mmkin' objects - 'saemix_model', 'saemix_data': Helper functions to fit nonlinear mixed-effects models for mmkin row objects using the saemix package diff --git a/R/nlme.mmkin.R b/R/nlme.mmkin.R index d3369cf5..6d24a044 100644 --- a/R/nlme.mmkin.R +++ b/R/nlme.mmkin.R @@ -42,6 +42,9 @@ get_deg_func <- function() { #' @importFrom stats na.fail as.formula #' @return Upon success, a fitted nlme.mmkin object, which is an nlme object #' with additional elements +#' @note As the object inherits from [nlme::nlme], there is a wealth of +#' methods that will automatically work on 'nlme.mmkin' objects, such as +#' [nlme::intervals()], [nlme::anova.lme()] and [nlme::coef.lme()]. #' @export #' @seealso \code{\link{nlme_function}} #' @examples @@ -141,8 +144,8 @@ nlme.mmkin <- function(model, data = sys.frame(sys.parent()), thisCall[["model"]] <- this_model - mean_dp <- mean_degparms(model) - dp_names <- names(mean_dp) + mean_dp_start <- mean_degparms(model) + dp_names <- names(mean_dp_start) thisCall[["data"]] <- nlme_data(model) @@ -175,10 +178,21 @@ nlme.mmkin <- function(model, data = sys.frame(sys.parent()), thisCall[["control"]] <- control } - val <- do.call("nlme.formula", thisCall) + fit_time <- system.time(val <- do.call("nlme.formula", thisCall)) + val$time <- fit_time + + val$mean_dp_start <- mean_dp_start val$mmkin_orig <- model val$data <- thisCall[["data"]] val$mkinmod <- model[[1]]$mkinmod + val$err_mode <- error_model + val$transform_rates <- model[[1]]$transform_rates + val$transform_fractions <- model[[1]]$transform_fractions + val$solution_type <- model[[1]]$solution_type + val$date.fit <- date() + val$nlmeversion <- as.character(utils::packageVersion("nlme")) + val$mkinversion <- as.character(utils::packageVersion("mkin")) + val$Rversion <- paste(R.version$major, R.version$minor, sep=".") class(val) <- c("nlme.mmkin", "nlme", "lme") return(val) } @@ -186,10 +200,30 @@ nlme.mmkin <- function(model, data = sys.frame(sys.parent()), #' @export #' @rdname nlme.mmkin #' @param x An nlme.mmkin object to print -#' @param ... Further arguments as in the generic print.nlme.mmkin <- function(x, ...) { - x$call$data <- "Not shown" - NextMethod("print", x) + cat( "Kinetic nonlinear mixed-effects model fit by " ) + cat( if(x$method == "REML") "REML\n" else "maximum likelihood\n") + cat("\nStructural model:\n") + diffs <- x$mmkin_orig[[1]]$mkinmod$diffs + nice_diffs <- gsub("^(d.*) =", "\\1/dt =", diffs) + writeLines(strwrap(nice_diffs, exdent = 11)) + cat("\nData:\n") + cat(nrow(x$data), "observations of", + length(unique(x$data$name)), "variable(s) grouped in", + length(unique(x$data$ds)), "datasets\n") + cat("\nLog-", if(x$method == "REML") "restricted-" else "", + "likelihood: ", format(x$logLik), "\n", sep = "") + fixF <- x$call$fixed + cat("\nFixed effects:\n", + deparse( + if(inherits(fixF, "formula") || is.call(fixF) || is.name(fixF)) + x$call$fixed + else + lapply(fixF, function(el) as.name(deparse(el)))), "\n") + print(fixef(x), ...) + cat("\n") + print(summary(x$modelStruct), sigma = x$sigma, ...) + invisible(x) } #' @export diff --git a/R/plot.nlme.mmkin.R b/R/plot.nlme.mmkin.R index afb682a7..05a17a22 100644 --- a/R/plot.nlme.mmkin.R +++ b/R/plot.nlme.mmkin.R @@ -11,6 +11,8 @@ if(getRversion() >= '2.15.1') utils::globalVariables("ds") #' @param rel.height.legend The relative height of the legend shown on top #' @param rel.height.bottom The relative height of the bottom plot row #' @param ymax Vector of maximum y axis values +#' @param ncol.legend Number of columns to use in the legend +#' @param nrow.legend Number of rows to use in the legend #' @param \dots Further arguments passed to \code{\link{plot.mkinfit}} and #' \code{\link{mkinresplot}}. #' @param resplot Should the residuals plotted against time or against @@ -28,7 +30,8 @@ if(getRversion() >= '2.15.1') utils::globalVariables("ds") #' names(ds) <- paste0("ds ", 6:10) #' dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"), #' A1 = mkinsub("SFO"), quiet = TRUE) -#' f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, cores = 1) +#' \dontrun{ +#' f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE) #' plot(f[, 3:4], standardized = TRUE) #' #' library(nlme) @@ -36,6 +39,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables("ds") #' # tolerance in order to speed up the fit for this example evaluation #' f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3)) #' plot(f_nlme) +#' } #' @export plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin_orig), obs_vars = names(x$mkinmod$map), diff --git a/R/sigma_twocomp.R b/R/sigma_twocomp.R index e8a92ced..e7f4368b 100644 --- a/R/sigma_twocomp.R +++ b/R/sigma_twocomp.R @@ -1,16 +1,16 @@ #' Two-component error model -#' +#' #' Function describing the standard deviation of the measurement error in #' dependence of the measured value \eqn{y}: -#' +#' #' \deqn{\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}} sigma = #' sqrt(sigma_low^2 + y^2 * rsd_high^2) -#' +#' #' This is the error model used for example by Werner et al. (1978). The model #' proposed by Rocke and Lorenzato (1995) can be written in this form as well, #' but assumes approximate lognormal distribution of errors for high values of #' y. -#' +#' #' @param y The magnitude of the observed value #' @param sigma_low The asymptotic minimum of the standard deviation for low #' observed values @@ -20,7 +20,7 @@ #' @references Werner, Mario, Brooks, Samuel H., and Knott, Lancaster B. (1978) #' Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry #' 24(11), 1895-1898. -#' +#' #' Rocke, David M. and Lorenzato, Stefan (1995) A two-component model for #' measurement error in analytical chemistry. Technometrics 37(2), 176-184. #' @examples @@ -36,15 +36,8 @@ #' data = d_syn, na.action = na.omit, #' start = list(parent_0 = 100, lrc = -3)) #' if (length(findFunction("varConstProp")) > 0) { -#' f_gnls_tc <- gnls(value ~ SSasymp(time, 0, parent_0, lrc), -#' data = d_syn, na.action = na.omit, -#' start = list(parent_0 = 100, lrc = -3), -#' weights = varConstProp()) -#' f_gnls_tc_sf <- gnls(value ~ SSasymp(time, 0, parent_0, lrc), -#' data = d_syn, na.action = na.omit, -#' start = list(parent_0 = 100, lrc = -3), -#' control = list(sigma = 1), -#' weights = varConstProp()) +#' f_gnls_tc <- update(f_gnls, weights = varConstProp()) +#' f_gnls_tc_sf <- update(f_gnls_tc, control = list(sigma = 1)) #' } #' f_mkin <- mkinfit("SFO", d_syn, error_model = "const", quiet = TRUE) #' f_mkin_tc <- mkinfit("SFO", d_syn, error_model = "tc", quiet = TRUE) diff --git a/R/summary.nlme.mmkin.R b/R/summary.nlme.mmkin.R new file mode 100644 index 00000000..9fdd3f73 --- /dev/null +++ b/R/summary.nlme.mmkin.R @@ -0,0 +1,233 @@ +#' Summary method for class "nlme.mmkin" +#' +#' Lists model equations, initial parameter values, optimised parameters +#' for fixed effects (population), random effects (deviations from the +#' population mean) and residual error model, as well as the resulting +#' endpoints such as formation fractions and DT50 values. Optionally +#' (default is FALSE), the data are listed in full. +#' +#' @param object an object of class [nlme.mmkin] +#' @param x an object of class [summary.nlme.mmkin] +#' @param data logical, indicating whether the full data should be included in +#' the summary. +#' @param verbose Should the summary be verbose? +#' @param distimes logical, indicating whether DT50 and DT90 values should be +#' included. +#' @param alpha error level for confidence interval estimation from the t +#' distribution +#' @param digits Number of digits to use for printing +#' @param \dots optional arguments passed to methods like \code{print}. +#' @return The summary function returns a list based on the [nlme] object +#' obtained in the fit, with at least the following additional components +#' \item{nlmeversion, mkinversion, Rversion}{The nlme, mkin and R versions used} +#' \item{date.fit, date.summary}{The dates where the fit and the summary were +#' produced} +#' \item{diffs}{The differential equations used in the degradation model} +#' \item{use_of_ff}{Was maximum or minimum use made of formation fractions} +#' \item{data}{The data} +#' \item{confint_trans}{Transformed parameters as used in the optimisation, with confidence intervals} +#' \item{confint_back}{Backtransformed parameters, with confidence intervals if available} +#' \item{ff}{The estimated formation fractions derived from the fitted +#' model.} +#' \item{distimes}{The DT50 and DT90 values for each observed variable.} +#' \item{SFORB}{If applicable, eigenvalues of SFORB components of the model.} +#' The print method is called for its side effect, i.e. printing the summary. +#' @importFrom stats predict +#' @author Johannes Ranke for the mkin specific parts +#' José Pinheiro and Douglas Bates for the components inherited from nlme +#' @examples +#' +#' # Generate five datasets following SFO kinetics +#' sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) +#' dt50_sfo_in_pop <- 50 +#' k_in_pop <- log(2) / dt50_sfo_in_pop +#' set.seed(1234) +#' k_in <- rlnorm(5, log(k_in_pop), 0.5) +#' SFO <- mkinmod(parent = mkinsub("SFO")) +#' +#' pred_sfo <- function(k) { +#' mkinpredict(SFO, +#' c(k_parent = k), +#' c(parent = 100), +#' sampling_times) +#' } +#' +#' ds_sfo_mean <- lapply(k_in, pred_sfo) +#' names(ds_sfo_mean) <- paste("ds", 1:5) +#' +#' ds_sfo_syn <- lapply(ds_sfo_mean, function(ds) { +#' add_err(ds, +#' sdfunc = function(value) sqrt(1^2 + value^2 * 0.07^2), +#' n = 1)[[1]] +#' }) +#' +#' # Evaluate using mmkin and nlme +#' library(nlme) +#' f_mmkin <- mmkin("SFO", ds_sfo_syn, quiet = TRUE, error_model = "tc", cores = 1) +#' f_nlme <- nlme(f_mmkin) +#' summary(f_nlme, data = TRUE) +#' +#' @export +summary.nlme.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes = TRUE, alpha = 0.05, ...) { + + mod_vars <- names(object$mkinmod$diffs) + + confint_trans <- intervals(object, which = "fixed", level = 1 - alpha)$fixed + attr(confint_trans, "label") <- NULL + pnames <- rownames(confint_trans) + confint_trans[, "est."] + bp <- backtransform_odeparms(confint_trans[, "est."], object$mkinmod, + object$transform_rates, object$transform_fractions) + bpnames <- names(bp) + + # variance-covariance estimates for fixed effects (from summary.lme) + fixed <- fixef(object) + stdFixed <- sqrt(diag(as.matrix(object$varFix))) + object$corFixed <- array( + t(object$varFix/stdFixed)/stdFixed, + dim(object$varFix), + list(names(fixed), names(fixed))) + + # Transform boundaries of CI for one parameter at a time, + # with the exception of sets of formation fractions (single fractions are OK). + f_names_skip <- character(0) + for (box in mod_vars) { # Figure out sets of fractions to skip + f_names <- grep(paste("^f", box, sep = "_"), pnames, value = TRUE) + n_paths <- length(f_names) + if (n_paths > 1) f_names_skip <- c(f_names_skip, f_names) + } + + confint_back <- matrix(NA, nrow = length(bp), ncol = 3, + dimnames = list(bpnames, colnames(confint_trans))) + confint_back[, "est."] <- bp + + for (pname in pnames) { + if (!pname %in% f_names_skip) { + par.lower <- confint_trans[pname, "lower"] + par.upper <- confint_trans[pname, "upper"] + names(par.lower) <- names(par.upper) <- pname + bpl <- backtransform_odeparms(par.lower, object$mkinmod, + object$transform_rates, + object$transform_fractions) + bpu <- backtransform_odeparms(par.upper, object$mkinmod, + object$transform_rates, + object$transform_fractions) + confint_back[names(bpl), "lower"] <- bpl + confint_back[names(bpu), "upper"] <- bpu + } + } + + object$confint_trans <- confint_trans + object$confint_back <- confint_back + + object$date.summary = date() + object$use_of_ff = object$mkinmod$use_of_ff + object$error_model_algorithm = object$mmkin_orig[[1]]$error_model_algorithm + err_mod = object$mmkin_orig[[1]]$err_mod + + object$diffs <- object$mkinmod$diffs + object$print_data <- data + if (data) { + object$data[["observed"]] <- object$data[["value"]] + object$data[["value"]] <- NULL + object$data[["predicted"]] <- predict(object) + object$data[["residual"]] <- residuals(object, type = "response") + object$data[["std"]] <- object$sigma <- 1/attr(object$modelStruct$varStruct, "weights") + object$data[["standardized"]] <- residuals(object, type = "pearson") + } + object$verbose <- verbose + + object$fixed <- object$mmkin_orig[[1]]$fixed + object$AIC = AIC(object) + object$BIC = BIC(object) + object$logLik = logLik(object) + + ep <- endpoints(object) + if (length(ep$ff) != 0) + object$ff <- ep$ff + if (distimes) object$distimes <- ep$distimes + if (length(ep$SFORB) != 0) object$SFORB <- ep$SFORB + class(object) <- c("summary.nlme.mmkin", "nlme.mmkin", "nlme", "lme") + return(object) +} + +#' @rdname summary.nlme.mmkin +#' @export +print.summary.nlme.mmkin <- function(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...) { + cat("nlme version used for fitting: ", x$nlmeversion, "\n") + cat("mkin version used for pre-fitting: ", x$mkinversion, "\n") + cat("R version used for fitting: ", x$Rversion, "\n") + + cat("Date of fit: ", x$date.fit, "\n") + cat("Date of summary:", x$date.summary, "\n") + + cat("\nEquations:\n") + nice_diffs <- gsub("^(d.*) =", "\\1/dt =", x[["diffs"]]) + writeLines(strwrap(nice_diffs, exdent = 11)) + + cat("\nData:\n") + cat(nrow(x$data), "observations of", + length(unique(x$data$name)), "variable(s) grouped in", + length(unique(x$data$ds)), "datasets\n") + + cat("\nModel predictions using solution type", x$solution_type, "\n") + + cat("\nFitted in", x$time[["elapsed"]], "s using", x$numIter, "iterations\n") + + cat("\nVariance model: ") + cat(switch(x$err_mod, + const = "Constant variance", + obs = "Variance unique to each observed variable", + tc = "Two-component variance function"), "\n") + + cat("\nMean of starting values for individual parameters:\n") + print(x$mean_dp_start) + + cat("\nFixed degradation parameter values:\n") + if(length(x$fixed$value) == 0) cat("None\n") + else print(x$fixed) + + cat("\nResults:\n\n") + print(data.frame(AIC = x$AIC, BIC = x$BIC, logLik = x$logLik, + row.names = " ")) + + cat("\nOptimised, transformed parameters with symmetric confidence intervals:\n") + print(x$confint_trans) + + if (nrow(x$confint_trans) > 1) { + corr <- x$corFixed + class(corr) <- "correlation" + print(corr, title = "\nCorrelation:", ...) + } + + cat("\nBacktransformed parameters with asymmetric confidence intervals:\n") + print(x$confint_back) + + print(summary(x$modelStruct), sigma = x$sigma, + reEstimates = x$coef$random, verbose = verbose, ...) + + printSFORB <- !is.null(x$SFORB) + if(printSFORB){ + cat("\nEstimated Eigenvalues of SFORB model(s):\n") + print(x$SFORB, digits=digits,...) + } + + printff <- !is.null(x$ff) + if(printff){ + cat("\nResulting formation fractions:\n") + print(data.frame(ff = x$ff), digits=digits,...) + } + + printdistimes <- !is.null(x$distimes) + if(printdistimes){ + cat("\nEstimated disappearance times:\n") + print(x$distimes, digits=digits,...) + } + + if (x$print_data){ + cat("\nData:\n") + print(format(x$data, digits = digits, ...), row.names = FALSE) + } + + invisible(x) +} diff --git a/_pkgdown.yml b/_pkgdown.yml index 4631dc97..ac100ac1 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -43,6 +43,7 @@ reference: contents: - nlme.mmkin - plot.nlme.mmkin + - summary.nlme.mmkin - nlme_function - get_deg_func - saemix_model diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index c29e413d..4e31f4b7 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -146,8 +146,7 @@ <a href="#mkin-0-9-50-4-unreleased" class="anchor"></a>mkin 0.9.50.4 (unreleased)<small> Unreleased </small> </h1> <ul> -<li><p>‘plot’ method for ‘nlme.mmkin’ objects</p></li> -<li><p>‘print’ method for ‘mmkin’ objects</p></li> +<li><p>‘plot’, ‘summary’ and ‘print’ methods for ‘nlme.mmkin’ objects</p></li> <li><p>‘saemix_model’, ‘saemix_data’: Helper functions to fit nonlinear mixed-effects models for mmkin row objects using the saemix package</p></li> </ul> </div> diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 8f493a24..657aa128 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2020-10-26T13:18Z +last_built: 2020-10-27T14:34Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png Binary files differindex cfc5bc2b..f001da49 100644 --- a/docs/dev/reference/Rplot001.png +++ b/docs/dev/reference/Rplot001.png diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index 24056025..fa3ec868 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -308,7 +308,7 @@ of an mmkin object</p></td> <tr> <th colspan="2"> <h2 id="section-mixed-models" class="hasAnchor"><a href="#section-mixed-models" class="anchor"></a>Mixed models</h2> - <p class="section-desc"><p>Create and work with nonlinear mixed models</p></p> + <p class="section-desc"><p>Create and work with nonlinear mixed effects models</p></p> </th> </tr> @@ -331,6 +331,12 @@ of an mmkin object</p></td> </tr><tr> <td> + <p><code><a href="summary.nlme.mmkin.html">summary(<i><nlme.mmkin></i>)</a></code> <code><a href="summary.nlme.mmkin.html">print(<i><summary.nlme.mmkin></i>)</a></code> </p> + </td> + <td><p>Summary method for class "nlme.mmkin"</p></td> + </tr><tr> + + <td> <p><code><a href="nlme.html">nlme_function()</a></code> <code><a href="nlme.html">mean_degparms()</a></code> <code><a href="nlme.html">nlme_data()</a></code> </p> </td> <td><p>Helper functions to create nlme models from mmkin row objects</p></td> diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html index 90aec9be..3fa4d97b 100644 --- a/docs/dev/reference/nlme.mmkin.html +++ b/docs/dev/reference/nlme.mmkin.html @@ -152,7 +152,7 @@ have been obtained by fitting the same model to a list of datasets.</p> </div> <pre class="usage"><span class='co'># S3 method for mmkin</span> -<span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span> +<span class='fu'>nlme</span><span class='op'>(</span> <span class='va'>model</span>, data <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.frame</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.parent</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>, <span class='va'>fixed</span>, @@ -255,6 +255,11 @@ parameters taken from the mmkin object are used</p></td> <p>Upon success, a fitted nlme.mmkin object, which is an nlme object with additional elements</p> + <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> + + <p>As the object inherits from <a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme::nlme</a>, there is a wealth of +methods that will automatically work on 'nlme.mmkin' objects, such as +<code><a href='https://rdrr.io/pkg/nlme/man/intervals.html'>nlme::intervals()</a></code>, <code><a href='https://rdrr.io/pkg/nlme/man/anova.lme.html'>nlme::anova.lme()</a></code> and <code><a href='https://rdrr.io/pkg/nlme/man/coef.lme.html'>nlme::coef.lme()</a></code>.</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <div class='dont-index'><p><code><a href='nlme_function.html'>nlme_function</a></code></p></div> @@ -270,11 +275,20 @@ with additional elements</p> </div><div class='output co'>#> df AIC #> f_nlme_sfo 5 625.0539 #> f_nlme_dfop 9 495.1270</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span> -</div><div class='output co'>#> Nonlinear mixed-effects model fit by maximum likelihood -#> Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k1, log_k2, g_ilr) -#> Data: "Not shown" -#> Log-likelihood: -238.5635 -#> Fixed: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) +</div><div class='output co'>#> Kinetic nonlinear mixed-effects model fit by maximum likelihood +#> +#> Structural model: +#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * +#> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) +#> * parent +#> +#> Data: +#> 90 observations of 1 variable(s) grouped in 5 datasets +#> +#> Log-likelihood: -238.5635 +#> +#> Fixed effects: +#> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) #> parent_0 log_k1 log_k2 g_ilr #> 94.17015133 -1.80015306 -4.14738870 0.02290935 #> @@ -284,9 +298,7 @@ with additional elements</p> #> Structure: Diagonal #> parent_0 log_k1 log_k2 g_ilr Residual #> StdDev: 2.488249 0.8447273 1.32965 0.3289311 2.321364 -#> -#> Number of Observations: 90 -#> Number of Groups: 5 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span> +#> </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span> </div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span> </div><div class='output co'>#> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 @@ -295,11 +307,18 @@ with additional elements</p> <span class='co'># \dontrun{</span> <span class='va'>f_nlme_2</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span>, start <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent_0 <span class='op'>=</span> <span class='fl'>100</span>, log_k_parent <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_nlme_2</span>, random <span class='op'>=</span> <span class='va'>parent_0</span> <span class='op'>~</span> <span class='fl'>1</span><span class='op'>)</span> -</div><div class='output co'>#> Nonlinear mixed-effects model fit by maximum likelihood -#> Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_parent) -#> Data: "Not shown" -#> Log-likelihood: -404.3729 -#> Fixed: list(parent_0 ~ 1, log_k_parent ~ 1) +</div><div class='output co'>#> Kinetic nonlinear mixed-effects model fit by maximum likelihood +#> +#> Structural model: +#> d_parent/dt = - k_parent * parent +#> +#> Data: +#> observations of 0 variable(s) grouped in 0 datasets +#> +#> Log-likelihood: -404.3729 +#> +#> Fixed effects: +#> list(parent_0 ~ 1, log_k_parent ~ 1) #> parent_0 log_k_parent #> 75.933480 -3.555983 #> @@ -307,9 +326,7 @@ with additional elements</p> #> Formula: parent_0 ~ 1 | ds #> parent_0 Residual #> StdDev: 0.002416792 21.63027 -#> -#> Number of Observations: 90 -#> Number of Groups: 5 </div><div class='input'> <span class='va'>ds_2</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>, +#> </div><div class='input'> <span class='va'>ds_2</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span> <span class='va'>m_sfo_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"A1"</span><span class='op'>)</span>, A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"min"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> @@ -395,11 +412,20 @@ with additional elements</p> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo</span>, <span class='va'>f_nlme_sfo_tc</span>, <span class='va'>f_nlme_dfop</span>, <span class='va'>f_nlme_dfop_tc</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_tc</span><span class='op'>)</span> <span class='op'>}</span> -</div><div class='output co'>#> Nonlinear mixed-effects model fit by maximum likelihood -#> Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k1, log_k2, g_ilr) -#> Data: "Not shown" -#> Log-likelihood: -238.4298 -#> Fixed: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) +</div><div class='output co'>#> Kinetic nonlinear mixed-effects model fit by maximum likelihood +#> +#> Structural model: +#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * +#> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) +#> * parent +#> +#> Data: +#> 90 observations of 1 variable(s) grouped in 5 datasets +#> +#> Log-likelihood: -238.4298 +#> +#> Fixed effects: +#> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) #> parent_0 log_k1 log_k2 g_ilr #> 94.04774463 -1.82339924 -4.16715509 0.04020161 #> @@ -415,19 +441,25 @@ with additional elements</p> #> Formula: ~fitted(.) #> Parameter estimates: #> const prop -#> 2.23222625 0.01262414 -#> Number of Observations: 90 -#> Number of Groups: 5 </div><div class='input'> +#> 2.23222625 0.01262414 </div><div class='input'> <span class='va'>f_2_obs</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo</span>, <span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>m_dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span> <span class='va'>f_nlme_sfo_sfo_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2_obs</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo_obs</span><span class='op'>)</span> -</div><div class='output co'>#> Nonlinear mixed-effects model fit by maximum likelihood -#> Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_parent_sink, log_k_parent_A1, log_k_A1_sink) -#> Data: "Not shown" -#> Log-likelihood: -472.976 -#> Fixed: list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1, log_k_A1_sink ~ 1) +</div><div class='output co'>#> Kinetic nonlinear mixed-effects model fit by maximum likelihood +#> +#> Structural model: +#> d_parent/dt = - k_parent_sink * parent - k_parent_A1 * parent +#> d_A1/dt = + k_parent_A1 * parent - k_A1_sink * A1 +#> +#> Data: +#> 170 observations of 2 variable(s) grouped in 5 datasets +#> +#> Log-likelihood: -472.976 +#> +#> Fixed effects: +#> list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1, log_k_A1_sink ~ 1) #> parent_0 log_k_parent_sink log_k_parent_A1 log_k_A1_sink #> 87.975536 -3.669816 -4.164127 -4.645073 #> @@ -443,9 +475,7 @@ with additional elements</p> #> Formula: ~1 | name #> Parameter estimates: #> parent A1 -#> 1.0000000 0.2050003 -#> Number of Observations: 170 -#> Number of Groups: 5 </div><div class='input'> <span class='co'># The same with DFOP-SFO does not converge, apparently the variances of</span> +#> 1.0000000 0.2050003 </div><div class='input'> <span class='co'># The same with DFOP-SFO does not converge, apparently the variances of</span> <span class='co'># parent and A1 are too similar in this case, so that the model is</span> <span class='co'># overparameterised</span> <span class='co'>#f_nlme_dfop_sfo_obs <- nlme(f_2_obs["DFOP-SFO", ], control = list(maxIter = 100))</span> diff --git a/docs/dev/reference/plot.nlme.mmkin.html b/docs/dev/reference/plot.nlme.mmkin.html index afd9d8d0..267bef05 100644 --- a/docs/dev/reference/plot.nlme.mmkin.html +++ b/docs/dev/reference/plot.nlme.mmkin.html @@ -215,6 +215,14 @@ predicted values?</p></td> scaling of the y axis and defaults to "auto".</p></td> </tr> <tr> + <th>ncol.legend</th> + <td><p>Number of columns to use in the legend</p></td> + </tr> + <tr> + <th>nrow.legend</th> + <td><p>Number of rows to use in the legend</p></td> + </tr> + <tr> <th>rel.height.legend</th> <td><p>The relative height of the legend shown on top</p></td> </tr> @@ -259,7 +267,8 @@ corresponding model prediction lines for the different datasets.</p></td> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='st'>"ds "</span>, <span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>)</span> <span class='va'>dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"A1"</span><span class='op'>)</span>, A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>f</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> +<span class='co'># \dontrun{</span> +<span class='va'>f</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> </div><div class='img'><img src='plot.nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://svn.r-project.org/R-packages/trunk/nlme/'>nlme</a></span><span class='op'>)</span> @@ -267,7 +276,8 @@ corresponding model prediction lines for the different datasets.</p></td> <span class='co'># tolerance in order to speed up the fit for this example evaluation</span> <span class='va'>f_nlme</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span>, control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>1e-3</span><span class='op'>)</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme</span><span class='op'>)</span> -</div><div class='img'><img src='plot.nlme.mmkin-2.png' alt='' width='700' height='433' /></div></pre> +</div><div class='img'><img src='plot.nlme.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> <nav id="toc" data-toggle="toc" class="sticky-top"> diff --git a/docs/dev/reference/sigma_twocomp.html b/docs/dev/reference/sigma_twocomp.html index ecea8499..8212e480 100644 --- a/docs/dev/reference/sigma_twocomp.html +++ b/docs/dev/reference/sigma_twocomp.html @@ -202,15 +202,8 @@ measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> data <span class='op'>=</span> <span class='va'>d_syn</span>, na.action <span class='op'>=</span> <span class='va'>na.omit</span>, start <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>parent_0 <span class='op'>=</span> <span class='fl'>100</span>, lrc <span class='op'>=</span> <span class='op'>-</span><span class='fl'>3</span><span class='op'>)</span><span class='op'>)</span> <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='fu'>findFunction</span><span class='op'>(</span><span class='st'>"varConstProp"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>></span> <span class='fl'>0</span><span class='op'>)</span> <span class='op'>{</span> - <span class='va'>f_gnls_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/gnls.html'>gnls</a></span><span class='op'>(</span><span class='va'>value</span> <span class='op'>~</span> <span class='fu'><a href='https://rdrr.io/r/stats/SSasymp.html'>SSasymp</a></span><span class='op'>(</span><span class='va'>time</span>, <span class='fl'>0</span>, <span class='va'>parent_0</span>, <span class='va'>lrc</span><span class='op'>)</span>, - data <span class='op'>=</span> <span class='va'>d_syn</span>, na.action <span class='op'>=</span> <span class='va'>na.omit</span>, - start <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>parent_0 <span class='op'>=</span> <span class='fl'>100</span>, lrc <span class='op'>=</span> <span class='op'>-</span><span class='fl'>3</span><span class='op'>)</span>, - weights <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/varConstProp.html'>varConstProp</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> - <span class='va'>f_gnls_tc_sf</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/gnls.html'>gnls</a></span><span class='op'>(</span><span class='va'>value</span> <span class='op'>~</span> <span class='fu'><a href='https://rdrr.io/r/stats/SSasymp.html'>SSasymp</a></span><span class='op'>(</span><span class='va'>time</span>, <span class='fl'>0</span>, <span class='va'>parent_0</span>, <span class='va'>lrc</span><span class='op'>)</span>, - data <span class='op'>=</span> <span class='va'>d_syn</span>, na.action <span class='op'>=</span> <span class='va'>na.omit</span>, - start <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>parent_0 <span class='op'>=</span> <span class='fl'>100</span>, lrc <span class='op'>=</span> <span class='op'>-</span><span class='fl'>3</span><span class='op'>)</span>, - control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>sigma <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>, - weights <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/varConstProp.html'>varConstProp</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> + <span class='va'>f_gnls_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_gnls</span>, weights <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/varConstProp.html'>varConstProp</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> + <span class='va'>f_gnls_tc_sf</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_gnls_tc</span>, control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>sigma <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>}</span> <span class='va'>f_mkin</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>d_syn</span>, error_model <span class='op'>=</span> <span class='st'>"const"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='va'>f_mkin_tc</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>d_syn</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> diff --git a/docs/dev/reference/summary.nlme.mmkin.html b/docs/dev/reference/summary.nlme.mmkin.html new file mode 100644 index 00000000..38f53122 --- /dev/null +++ b/docs/dev/reference/summary.nlme.mmkin.html @@ -0,0 +1,446 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Summary method for class "nlme.mmkin" — summary.nlme.mmkin • mkin</title> + + +<!-- jquery --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" 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headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + + + + +<meta property="og:title" content="Summary method for class "nlme.mmkin" — summary.nlme.mmkin" /> +<meta property="og:description" content="Lists model equations, initial parameter values, optimised parameters +for fixed effects (population), random effects (deviations from the +population mean) and residual error model, as well as the resulting +endpoints such as formation fractions and DT50 values. Optionally +(default is FALSE), the data are listed in full." /> + + +<meta name="robots" content="noindex"> + +<!-- mathjax --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + + + + </head> + + <body data-spy="scroll" data-target="#toc"> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + </li> + </ul> +</li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header> + +<div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Summary method for class "nlme.mmkin"</h1> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/summary.nlme.mmkin.R'><code>R/summary.nlme.mmkin.R</code></a></small> + <div class="hidden name"><code>summary.nlme.mmkin.Rd</code></div> + </div> + + <div class="ref-description"> + <p>Lists model equations, initial parameter values, optimised parameters +for fixed effects (population), random effects (deviations from the +population mean) and residual error model, as well as the resulting +endpoints such as formation fractions and DT50 values. Optionally +(default is FALSE), the data are listed in full.</p> + </div> + + <pre class="usage"><span class='co'># S3 method for nlme.mmkin</span> +<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span> + <span class='va'>object</span>, + data <span class='op'>=</span> <span class='cn'>FALSE</span>, + verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, + distimes <span class='op'>=</span> <span class='cn'>TRUE</span>, + alpha <span class='op'>=</span> <span class='fl'>0.05</span>, + <span class='va'>...</span> +<span class='op'>)</span> + +<span class='co'># S3 method for summary.nlme.mmkin</span> +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, digits <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"digits"</span><span class='op'>)</span> <span class='op'>-</span> <span class='fl'>3</span><span class='op'>)</span>, verbose <span class='op'>=</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>verbose</span>, <span class='va'>...</span><span class='op'>)</span></pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>object</th> + <td><p>an object of class <a href='nlme.mmkin.html'>nlme.mmkin</a></p></td> + </tr> + <tr> + <th>data</th> + <td><p>logical, indicating whether the full data should be included in +the summary.</p></td> + </tr> + <tr> + <th>verbose</th> + <td><p>Should the summary be verbose?</p></td> + </tr> + <tr> + <th>distimes</th> + <td><p>logical, indicating whether DT50 and DT90 values should be +included.</p></td> + </tr> + <tr> + <th>alpha</th> + <td><p>error level for confidence interval estimation from the t +distribution</p></td> + </tr> + <tr> + <th>...</th> + <td><p>optional arguments passed to methods like <code>print</code>.</p></td> + </tr> + <tr> + <th>x</th> + <td><p>an object of class summary.nlme.mmkin</p></td> + </tr> + <tr> + <th>digits</th> + <td><p>Number of digits to use for printing</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>The summary function returns a list based on the <a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a> object +obtained in the fit, with at least the following additional components</p> +<dt>nlmeversion, mkinversion, Rversion</dt><dd><p>The nlme, mkin and R versions used</p></dd> +<dt>date.fit, date.summary</dt><dd><p>The dates where the fit and the summary were +produced</p></dd> +<dt>diffs</dt><dd><p>The differential equations used in the degradation model</p></dd> +<dt>use_of_ff</dt><dd><p>Was maximum or minimum use made of formation fractions</p></dd> +<dt>data</dt><dd><p>The data</p></dd> +<dt>confint_trans</dt><dd><p>Transformed parameters as used in the optimisation, with confidence intervals</p></dd> +<dt>confint_back</dt><dd><p>Backtransformed parameters, with confidence intervals if available</p></dd> +<dt>ff</dt><dd><p>The estimated formation fractions derived from the fitted +model.</p></dd> +<dt>distimes</dt><dd><p>The DT50 and DT90 values for each observed variable.</p></dd> +<dt>SFORB</dt><dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd> +The print method is called for its side effect, i.e. printing the summary. + + <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> + + <p>Johannes Ranke for the mkin specific parts +José Pinheiro and Douglas Bates for the components inherited from nlme</p> + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'> +<span class='co'># Generate five datasets following SFO kinetics</span> +<span class='va'>sampling_times</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span> +<span class='va'>dt50_sfo_in_pop</span> <span class='op'><-</span> <span class='fl'>50</span> +<span class='va'>k_in_pop</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span> <span class='op'>/</span> <span class='va'>dt50_sfo_in_pop</span> +<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>1234</span><span class='op'>)</span> +<span class='va'>k_in</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Lognormal.html'>rlnorm</a></span><span class='op'>(</span><span class='fl'>5</span>, <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='va'>k_in_pop</span><span class='op'>)</span>, <span class='fl'>0.5</span><span class='op'>)</span> +<span class='va'>SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> + +<span class='va'>pred_sfo</span> <span class='op'><-</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>k</span><span class='op'>)</span> <span class='op'>{</span> + <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>SFO</span>, + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='va'>k</span><span class='op'>)</span>, + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, + <span class='va'>sampling_times</span><span class='op'>)</span> +<span class='op'>}</span> + +<span class='va'>ds_sfo_mean</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>k_in</span>, <span class='va'>pred_sfo</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds_sfo_mean</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"ds"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>5</span><span class='op'>)</span> + +<span class='va'>ds_sfo_syn</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>ds_sfo_mean</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'>{</span> + <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>ds</span>, + sdfunc <span class='op'>=</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>sqrt</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>+</span> <span class='va'>value</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>*</span> <span class='fl'>0.07</span><span class='op'>^</span><span class='fl'>2</span><span class='op'>)</span>, + n <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span> +<span class='op'>}</span><span class='op'>)</span> + +<span class='co'># Evaluate using mmkin and nlme</span> +<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://svn.r-project.org/R-packages/trunk/nlme/'>nlme</a></span><span class='op'>)</span> +<span class='va'>f_mmkin</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>ds_sfo_syn</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.00371</span></div><div class='input'><span class='va'>f_nlme</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>)</span> +</div><div class='output co'>#> <span class='warning'>Warning: Iteration 3, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>f_nlme</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='output co'>#> nlme version used for fitting: 3.1.150.1 +#> mkin version used for pre-fitting: 0.9.50.4 +#> R version used for fitting: 4.0.3 +#> Date of fit: Tue Oct 27 15:25:23 2020 +#> Date of summary: Tue Oct 27 15:25:23 2020 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> +#> Data: +#> 90 observations of 1 variable(s) grouped in 5 datasets +#> +#> Model predictions using solution type analytical +#> +#> Fitted in 0.581 s using 5 iterations +#> +#> Variance model: Two-component variance function +#> +#> Mean of starting values for individual parameters: +#> parent_0 log_k_parent +#> 97.849556 -4.455036 +#> +#> Fixed degradation parameter values: +#> None +#> +#> Results: +#> +#> AIC BIC logLik +#> 555.792 570.7908 -271.896 +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> lower est. upper +#> parent_0 94.701336 97.763446 100.82556 +#> log_k_parent -5.007574 -4.461767 -3.91596 +#> +#> Correlation: +#> prnt_0 +#> log_k_parent 0.024 +#> +#> Backtransformed parameters with asymmetric confidence intervals: +#> lower est. upper +#> parent_0 94.701335804 97.76344625 100.82555670 +#> k_parent 0.006687109 0.01154195 0.01992142 +#> Random effects: +#> Formula: list(parent_0 ~ 1, log_k_parent ~ 1) +#> Level: ds +#> Structure: Diagonal +#> parent_0 log_k_parent Residual +#> StdDev: 16.65969 3.516961 5.709013 +#> +#> Variance function: +#> Structure: Constant plus proportion of variance covariate +#> Formula: ~fitted(.) +#> Parameter estimates: +#> const prop +#> 1.55075176 0.05680853 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 60.05 199.5 +#> +#> Data: +#> ds name time observed predicted residual std standardized +#> ds 1 parent 0 103.6 97.42 6.17540 5.748 1.074413 +#> ds 1 parent 0 95.9 97.42 -1.52460 5.748 -0.265253 +#> ds 1 parent 1 95.4 96.72 -1.31719 5.709 -0.230721 +#> ds 1 parent 1 95.3 96.72 -1.41719 5.709 -0.248237 +#> ds 1 parent 3 91.6 95.32 -3.71774 5.633 -0.660046 +#> ds 1 parent 3 94.5 95.32 -0.81774 5.633 -0.145181 +#> ds 1 parent 7 88.1 92.58 -4.47930 5.483 -0.816920 +#> ds 1 parent 7 89.6 92.58 -2.97930 5.483 -0.543355 +#> ds 1 parent 14 90.3 87.97 2.32502 5.233 0.444318 +#> ds 1 parent 14 96.0 87.97 8.02502 5.233 1.533602 +#> ds 1 parent 28 80.2 79.44 0.75809 4.772 0.158862 +#> ds 1 parent 28 77.9 79.44 -1.54191 4.772 -0.323118 +#> ds 1 parent 60 59.3 62.92 -3.61742 3.896 -0.928458 +#> ds 1 parent 60 59.6 62.92 -3.31742 3.896 -0.851459 +#> ds 1 parent 90 59.4 50.56 8.83825 3.264 2.707613 +#> ds 1 parent 90 51.0 50.56 0.43825 3.264 0.134260 +#> ds 1 parent 120 38.8 40.63 -1.83247 2.781 -0.658968 +#> ds 1 parent 120 38.9 40.63 -1.73247 2.781 -0.623007 +#> ds 2 parent 0 103.2 97.17 6.02995 5.734 1.051655 +#> ds 2 parent 0 95.1 97.17 -2.07005 5.734 -0.361027 +#> ds 2 parent 1 88.3 95.59 -7.28901 5.647 -1.290694 +#> ds 2 parent 1 102.4 95.59 6.81099 5.647 1.206048 +#> ds 2 parent 3 88.4 92.50 -4.10371 5.479 -0.748984 +#> ds 2 parent 3 95.2 92.50 2.69629 5.479 0.492110 +#> ds 2 parent 7 83.5 86.63 -3.12863 5.160 -0.606349 +#> ds 2 parent 7 96.4 86.63 9.77137 5.160 1.893751 +#> ds 2 parent 14 77.3 77.23 0.06920 4.653 0.014871 +#> ds 2 parent 14 76.0 77.23 -1.23080 4.653 -0.264497 +#> ds 2 parent 28 61.7 61.38 0.31692 3.816 0.083043 +#> ds 2 parent 28 56.5 61.38 -4.88308 3.816 -1.279513 +#> ds 2 parent 60 35.1 36.31 -1.21343 2.581 -0.470178 +#> ds 2 parent 60 32.2 36.31 -4.11343 2.581 -1.593868 +#> ds 2 parent 90 21.2 22.20 -0.99906 1.999 -0.499832 +#> ds 2 parent 90 23.3 22.20 1.10094 1.999 0.550800 +#> ds 2 parent 120 14.1 13.57 0.52931 1.732 0.305638 +#> ds 2 parent 120 16.9 13.57 3.32931 1.732 1.922443 +#> ds 3 parent 0 92.4 94.12 -1.71979 5.567 -0.308917 +#> ds 3 parent 0 94.0 94.12 -0.11979 5.567 -0.021517 +#> ds 3 parent 1 95.7 91.97 3.72634 5.450 0.683712 +#> ds 3 parent 1 90.8 91.97 -1.17366 5.450 -0.215343 +#> ds 3 parent 3 86.7 87.83 -1.12709 5.225 -0.215720 +#> ds 3 parent 3 85.8 87.83 -2.02709 5.225 -0.387976 +#> ds 3 parent 7 77.1 80.09 -2.98635 4.807 -0.621300 +#> ds 3 parent 7 81.5 80.09 1.41365 4.807 0.294104 +#> ds 3 parent 14 69.1 68.15 0.95467 4.170 0.228922 +#> ds 3 parent 14 62.4 68.15 -5.74533 4.170 -1.377682 +#> ds 3 parent 28 49.1 49.34 -0.23911 3.203 -0.074644 +#> ds 3 parent 28 47.2 49.34 -2.13911 3.203 -0.667787 +#> ds 3 parent 60 21.9 23.58 -1.68477 2.049 -0.822090 +#> ds 3 parent 60 23.6 23.58 0.01523 2.049 0.007431 +#> ds 3 parent 90 12.4 11.81 0.59388 1.690 0.351500 +#> ds 3 parent 90 13.8 11.81 1.99388 1.690 1.180112 +#> ds 3 parent 120 4.9 5.91 -1.00993 1.587 -0.636506 +#> ds 3 parent 120 7.5 5.91 1.59007 1.587 1.002137 +#> ds 4 parent 0 91.8 101.72 -9.92097 5.983 -1.658171 +#> ds 4 parent 0 104.6 101.72 2.87903 5.983 0.481194 +#> ds 4 parent 1 117.5 101.27 16.23017 5.958 2.723944 +#> ds 4 parent 1 99.3 101.27 -1.96983 5.958 -0.330602 +#> ds 4 parent 3 94.0 100.37 -6.37355 5.909 -1.078583 +#> ds 4 parent 3 98.7 100.37 -1.67355 5.909 -0.283212 +#> ds 4 parent 7 109.2 98.60 10.59529 5.812 1.822915 +#> ds 4 parent 7 89.2 98.60 -9.40471 5.812 -1.618075 +#> ds 4 parent 14 103.3 95.58 7.71609 5.647 1.366386 +#> ds 4 parent 14 103.0 95.58 7.41609 5.647 1.313261 +#> ds 4 parent 28 90.8 89.82 0.98290 5.333 0.184310 +#> ds 4 parent 28 88.7 89.82 -1.11710 5.333 -0.209477 +#> ds 4 parent 60 74.8 77.91 -3.10870 4.690 -0.662879 +#> ds 4 parent 60 75.3 77.91 -2.60870 4.690 -0.556262 +#> ds 4 parent 90 71.1 68.18 2.91738 4.172 0.699234 +#> ds 4 parent 90 78.0 68.18 9.81738 4.172 2.353017 +#> ds 4 parent 120 59.1 59.67 -0.57073 3.728 -0.153107 +#> ds 4 parent 120 53.8 59.67 -5.87073 3.728 -1.574902 +#> ds 5 parent 0 94.9 98.38 -3.48183 5.800 -0.600307 +#> ds 5 parent 0 101.8 98.38 3.41817 5.800 0.589332 +#> ds 5 parent 1 96.1 96.75 -0.65141 5.711 -0.114065 +#> ds 5 parent 1 97.1 96.75 0.34859 5.711 0.061040 +#> ds 5 parent 3 93.8 93.57 0.22881 5.537 0.041323 +#> ds 5 parent 3 85.8 93.57 -7.77119 5.537 -1.403444 +#> ds 5 parent 7 87.6 87.52 0.07909 5.208 0.015186 +#> ds 5 parent 7 94.0 87.52 6.47909 5.208 1.244026 +#> ds 5 parent 14 82.5 77.86 4.64101 4.687 0.990182 +#> ds 5 parent 14 81.7 77.86 3.84101 4.687 0.819498 +#> ds 5 parent 28 60.0 61.62 -1.61729 3.829 -0.422433 +#> ds 5 parent 28 61.0 61.62 -0.61729 3.829 -0.161236 +#> ds 5 parent 60 32.5 36.10 -3.59608 2.571 -1.398750 +#> ds 5 parent 60 35.5 36.10 -0.59608 2.571 -0.231854 +#> ds 5 parent 90 21.8 21.86 -0.06415 1.987 -0.032287 +#> ds 5 parent 90 24.4 21.86 2.53585 1.987 1.276317 +#> ds 5 parent 120 14.1 13.24 0.85643 1.724 0.496877 +#> ds 5 parent 120 12.1 13.24 -1.14357 1.724 -0.663473</div><div class='input'> +</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"> + <h2 data-toc-skip>Contents</h2> + </nav> + </div> +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + diff --git a/docs/dev/sitemap.xml b/docs/dev/sitemap.xml index 8c4d8cbe..67e100de 100644 --- a/docs/dev/sitemap.xml +++ b/docs/dev/sitemap.xml @@ -187,6 +187,9 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/summary.mkinfit.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/summary.nlme.mmkin.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/synthetic_data_for_UBA_2014.html</loc> </url> <url> diff --git a/man/nlme.mmkin.Rd b/man/nlme.mmkin.Rd index 041b939a..bf45c6e5 100644 --- a/man/nlme.mmkin.Rd +++ b/man/nlme.mmkin.Rd @@ -74,6 +74,11 @@ This functions sets up a nonlinear mixed effects model for an mmkin row object. An mmkin row object is essentially a list of mkinfit objects that have been obtained by fitting the same model to a list of datasets. } +\note{ +As the object inherits from \link[nlme:nlme]{nlme::nlme}, there is a wealth of +methods that will automatically work on 'nlme.mmkin' objects, such as +\code{\link[nlme:intervals]{nlme::intervals()}}, \code{\link[nlme:anova.lme]{nlme::anova.lme()}} and \code{\link[nlme:coef.lme]{nlme::coef.lme()}}. +} \examples{ ds <- lapply(experimental_data_for_UBA_2019[6:10], function(x) subset(x$data[c("name", "time", "value")], name == "parent")) diff --git a/man/plot.nlme.mmkin.Rd b/man/plot.nlme.mmkin.Rd index 6944d4b1..5f0f0ef1 100644 --- a/man/plot.nlme.mmkin.Rd +++ b/man/plot.nlme.mmkin.Rd @@ -50,6 +50,10 @@ predicted values?} \item{maxabs}{Maximum absolute value of the residuals. This is used for the scaling of the y axis and defaults to "auto".} +\item{ncol.legend}{Number of columns to use in the legend} + +\item{nrow.legend}{Number of rows to use in the legend} + \item{rel.height.legend}{The relative height of the legend shown on top} \item{rel.height.bottom}{The relative height of the bottom plot row} @@ -78,7 +82,8 @@ ds <- lapply(experimental_data_for_UBA_2019[6:10], names(ds) <- paste0("ds ", 6:10) dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"), A1 = mkinsub("SFO"), quiet = TRUE) -f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, cores = 1) +\dontrun{ +f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE) plot(f[, 3:4], standardized = TRUE) library(nlme) @@ -87,6 +92,7 @@ library(nlme) f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3)) plot(f_nlme) } +} \author{ Johannes Ranke } diff --git a/man/sigma_twocomp.Rd b/man/sigma_twocomp.Rd index ed79d493..d205a2f7 100644 --- a/man/sigma_twocomp.Rd +++ b/man/sigma_twocomp.Rd @@ -44,15 +44,8 @@ f_gnls <- gnls(value ~ SSasymp(time, 0, parent_0, lrc), data = d_syn, na.action = na.omit, start = list(parent_0 = 100, lrc = -3)) if (length(findFunction("varConstProp")) > 0) { - f_gnls_tc <- gnls(value ~ SSasymp(time, 0, parent_0, lrc), - data = d_syn, na.action = na.omit, - start = list(parent_0 = 100, lrc = -3), - weights = varConstProp()) - f_gnls_tc_sf <- gnls(value ~ SSasymp(time, 0, parent_0, lrc), - data = d_syn, na.action = na.omit, - start = list(parent_0 = 100, lrc = -3), - control = list(sigma = 1), - weights = varConstProp()) + f_gnls_tc <- update(f_gnls, weights = varConstProp()) + f_gnls_tc_sf <- update(f_gnls_tc, control = list(sigma = 1)) } f_mkin <- mkinfit("SFO", d_syn, error_model = "const", quiet = TRUE) f_mkin_tc <- mkinfit("SFO", d_syn, error_model = "tc", quiet = TRUE) diff --git a/man/summary.nlme.mmkin.Rd b/man/summary.nlme.mmkin.Rd new file mode 100644 index 00000000..ea625dd7 --- /dev/null +++ b/man/summary.nlme.mmkin.Rd @@ -0,0 +1,99 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/summary.nlme.mmkin.R +\name{summary.nlme.mmkin} +\alias{summary.nlme.mmkin} +\alias{print.summary.nlme.mmkin} +\title{Summary method for class "nlme.mmkin"} +\usage{ +\method{summary}{nlme.mmkin}( + object, + data = FALSE, + verbose = FALSE, + distimes = TRUE, + alpha = 0.05, + ... +) + +\method{print}{summary.nlme.mmkin}(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...) +} +\arguments{ +\item{object}{an object of class \link{nlme.mmkin}} + +\item{data}{logical, indicating whether the full data should be included in +the summary.} + +\item{verbose}{Should the summary be verbose?} + +\item{distimes}{logical, indicating whether DT50 and DT90 values should be +included.} + +\item{alpha}{error level for confidence interval estimation from the t +distribution} + +\item{\dots}{optional arguments passed to methods like \code{print}.} + +\item{x}{an object of class \link{summary.nlme.mmkin}} + +\item{digits}{Number of digits to use for printing} +} +\value{ +The summary function returns a list based on the \link{nlme} object +obtained in the fit, with at least the following additional components +\item{nlmeversion, mkinversion, Rversion}{The nlme, mkin and R versions used} +\item{date.fit, date.summary}{The dates where the fit and the summary were +produced} +\item{diffs}{The differential equations used in the degradation model} +\item{use_of_ff}{Was maximum or minimum use made of formation fractions} +\item{data}{The data} +\item{confint_trans}{Transformed parameters as used in the optimisation, with confidence intervals} +\item{confint_back}{Backtransformed parameters, with confidence intervals if available} +\item{ff}{The estimated formation fractions derived from the fitted +model.} +\item{distimes}{The DT50 and DT90 values for each observed variable.} +\item{SFORB}{If applicable, eigenvalues of SFORB components of the model.} +The print method is called for its side effect, i.e. printing the summary. +} +\description{ +Lists model equations, initial parameter values, optimised parameters +for fixed effects (population), random effects (deviations from the +population mean) and residual error model, as well as the resulting +endpoints such as formation fractions and DT50 values. Optionally +(default is FALSE), the data are listed in full. +} +\examples{ + +# Generate five datasets following SFO kinetics +sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) +dt50_sfo_in_pop <- 50 +k_in_pop <- log(2) / dt50_sfo_in_pop +set.seed(1234) +k_in <- rlnorm(5, log(k_in_pop), 0.5) +SFO <- mkinmod(parent = mkinsub("SFO")) + +pred_sfo <- function(k) { + mkinpredict(SFO, + c(k_parent = k), + c(parent = 100), + sampling_times) +} + +ds_sfo_mean <- lapply(k_in, pred_sfo) +names(ds_sfo_mean) <- paste("ds", 1:5) + +ds_sfo_syn <- lapply(ds_sfo_mean, function(ds) { + add_err(ds, + sdfunc = function(value) sqrt(1^2 + value^2 * 0.07^2), + n = 1)[[1]] +}) + +# Evaluate using mmkin and nlme +library(nlme) +f_mmkin <- mmkin("SFO", ds_sfo_syn, quiet = TRUE, error_model = "tc", cores = 1) +f_nlme <- nlme(f_mmkin) +summary(f_nlme, data = TRUE) + +} +\author{ +Johannes Ranke for the mkin specific parts +José Pinheiro and Douglas Bates for the components inherited from nlme +} @@ -5,19 +5,19 @@ Testing mkin ✔ | 2 | Export dataset for reading into CAKE ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.9 s] ✔ | 4 | Calculation of FOCUS chi2 error levels [0.4 s] -✔ | 7 | Fitting the SFORB model [3.3 s] -✔ | 5 | Analytical solutions for coupled models [3.1 s] +✔ | 7 | Fitting the SFORB model [3.4 s] +✔ | 5 | Analytical solutions for coupled models [3.2 s] ✔ | 5 | Calculation of Akaike weights ✔ | 10 | Confidence intervals and p-values [1.0 s] -✔ | 14 | Error model fitting [3.6 s] -✔ | 4 | Test fitting the decline of metabolites from their maximum [0.2 s] +✔ | 14 | Error model fitting [4.2 s] +✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3 s] ✔ | 1 | Fitting the logistic model [0.2 s] ✔ | 1 | Test dataset class mkinds used in gmkin ✔ | 1 | mkinfit features [0.2 s] ✔ | 12 | Special cases of mkinfit calls [0.6 s] ✔ | 8 | mkinmod model generation and printing [0.2 s] ✔ | 3 | Model predictions with mkinpredict [0.4 s] -✔ | 14 2 | Evaluations according to 2015 NAFTA guidance [1.0 s] +✔ | 14 2 | Evaluations according to 2015 NAFTA guidance [1.2 s] ──────────────────────────────────────────────────────────────────────────────── test_nafta.R:25: skip: Test data from Appendix B are correctly evaluated Reason: getRversion() < "4.1.0" is TRUE @@ -25,8 +25,8 @@ Reason: getRversion() < "4.1.0" is TRUE test_nafta.R:53: skip: Test data from Appendix D are correctly evaluated Reason: getRversion() < "4.1.0" is TRUE ──────────────────────────────────────────────────────────────────────────────── -✔ | 9 | Nonlinear mixed-effects models [7.7 s] -✔ | 0 1 | Plotting [0.6 s] +✔ | 9 | Nonlinear mixed-effects models [7.8 s] +✔ | 0 1 | Plotting [0.7 s] ──────────────────────────────────────────────────────────────────────────────── test_plot.R:24: skip: Plotting mkinfit and mmkin objects is reproducible Reason: getRversion() < "4.1.0" is TRUE @@ -35,12 +35,12 @@ Reason: getRversion() < "4.1.0" is TRUE ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5 s] ✔ | 4 | Summary [0.1 s] ✔ | 1 | Summaries of old mkinfit objects -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1 s] -✔ | 9 | Hypothesis tests [6.6 s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2 s] +✔ | 9 | Hypothesis tests [6.7 s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.5 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 36.5 s +Duration: 37.8 s OK: 146 Failed: 0 diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf index 115d28f4..b8828b57 100644 --- a/tests/testthat/FOCUS_2006_D.csf +++ b/tests/testthat/FOCUS_2006_D.csf @@ -5,7 +5,7 @@ Description: MeasurementUnits: % AR TimeUnits: days Comments: Created using mkin::CAKE_export -Date: 2020-10-08 +Date: 2020-10-27 Optimiser: IRLS [Data] |
